Fileinput Exploration with Pandas and Plotly
Contents
Fileinput Exploration with Pandas and Plotly#
In Panel the FileDownload widget allows downloading a file generated on the server the app is running on while the FileInput widget allows uploading a file. In this example we demonstrate a pipeline of two little apps one which allows generating a sample data CSV file and one which allows uploading this file and displays it as a Plotly plot.
For more details on how to use these components see FileInput and FileDownload reference guides.
import io
import param
import panel as pn
import pandas as pd
import random
import json
from standard_workflows import analysis_params as ap
from datetime import datetime, timedelta
import plotly.express as px
pn.extension('plotly', 'tabulator', sizing_mode="stretch_width")
pn.extension('ace', 'jsoneditor')
Lets start out by creating some sample data by defining some parameters which declare bounds on the values to generate along with a FileDownload widget which will allow the user to download the data onto their machine.
class colors:
HEADER = '\033[95m'
OKBLUE = '\033[94m'
OKCYAN = '\033[96m'
OKGREEN = '\033[92m'
WARNING = '\033[93m'
FAIL = '\033[91m'
ENDC = '\033[0m'
BOLD = '\033[1m'
UNDERLINE = '\033[4m'
print(f"{colors.WARNING}Warning: No active frommets remain. Continue?{colors.ENDC}")
# not working
from termcolor import colored
print(colored('hello', 'red'))
Warning: No active frommets remain. Continue?
hello
class AnalysisInit(param.Parameterized): # Basic paramters to set projName = pn.widgets.TextInput(name = ‘Full Project Name’, placeholder = ‘aNameWithoutSpaces’) projID = pn.widgets.TextInput(name = ‘Project ID ‘, placeholder = ‘two to six capital letters’) version = pn.widgets.TextInput(name = ‘Analysis Version’, placeholder = ‘v01’) host = pn.widgets.Select(name = ‘Host’, default=”human”, options=[‘human’, ‘mouse’]) datasetname = pn.widgets.TextInput(name = “Dataset Name”, placeholder = ‘all_tumor_liver_pid12pid14’) seqType = pn.widgets.Select(name = ‘Sequencing Type’, default = ‘sc’, options=[‘sc’, ‘sn’, ‘atac’, ‘bulk’]) local_folder_path = pn.widgets.TextInput(name = ‘Results Folder Path’, placeholder = ‘path to where to save the results folder’) # Put elements into grid proj_parameters = pn.GridBox(projName, projID, version, host, datasetname, seqType, local_folder_path, ncols = 2) # Param Editor param_editor = pn.widgets.JSONEditor(value= ap.analysis_params, width=400, height=800) # File Handling add_data = pn.widgets.FileInput() upload_params = pn.widgets.FileInput()
data = ''
#setup_analysis = param.Action(lambda self: save_params(), label=”Run Analysis Setup”, doc=”””
An action callback which will initialize the analysis obj.”””)#
def do_save_params(self):
"""
A FileDownload callback will return a file-like object which can be serialized
and sent to the client.
"""
import yaml
ff = open(os.path.join(local_folder_path.value, projID.value, version.value, host,value, seqType.value, datasetname.value, 'data', 'data.h5ad'), 'w+')
yaml.dump(json_editor.value, ff)
#self.download.filename = file_name
#sio = io.StringIO()
#sample_df.to_csv(sio, index=False)
#sio.seek(0)
#return sio
save_params = pn.widgets.FileDownload(name = 'Save Parameters', filename = 'analysis_params.yaml', callback = do_save_params, button_type = 'primary')
def __init__(self, **params):
super().__init__(**params)
# table = pn.widgets.Tabulator(
# pd.DataFrame(self.analysis_params), layout='fit_data_stretch', theme='site', height=360
#)
def _add_data():
if add_data.value is not None:
import scanpy
self.data = scanpy.read_h5ad(add_data.value)
ff = open(os.path.join(local_folder_path, projName.value, self.download.file_name), 'w+')
yaml.dump(self.data, ff)
analysis_init = AnalysisInit() pn.Column(pn.Row(analysis_init, analysis_init.param_editor), pn.Row(analysis_init.proj_parameters))
pn.widgets.TextInput(name = ‘Full Project Name’, placeholder = ‘aNameWithoutSpaces’)
pn.widgets.Select(name = ‘Sequencing Type’, default = ‘sc’, options=[‘sc’, ‘sn’, ‘atac’, ‘bulk’])
pn.GridBox(projName, projID, version, host, datasetname, ncols = 2)
pn.widgets.JSONEditor(value= ap.analysis_params, width=400, height=800)
pn.widgets.Tabulator(pd.DataFrame(self.analysis_params), layout=’fit_data_stretch’, theme=’site’, height=360)
add_data = pn.widgets.Button(name=’Click me’, button_type=’primary’)
add_data.on_click(_add_data)
param Action Button
action = param.Action(lambda x: x.param.trigger(‘action’), label=’Click here!’)
number = param.Integer(default=0)
@param.depends(‘action’)
def get_number(self):
self.number += 1
return self.number
“””
A FileDownload callback will return a file-like object which can be serialized
and sent to the client.
“””
self.download.filename = self.file_name
sio = io.StringIO()
self.sample_df.to_csv(sio, index=False)
sio.seek(0)
return sio
import scanpy
d = scanpy.read_h5ad('Users/hanna/Documents/projects/MBEN/all_cnvsNormal/data/all_cnvsNormal.h5ad')
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
Cell In [61], line 2
1 import scanpy
----> 2 d = scanpy.read_h5ad('Users/hanna/Documents/projects/MBEN/all_cnvsNormal/data/all_cnvsNormal.h5ad')
File ~/Library/Caches/pypoetry/virtualenvs/standard-workflows-7zflNV5z-py3.9/lib/python3.9/site-packages/anndata/_io/h5ad.py:224, in read_h5ad(filename, backed, as_sparse, as_sparse_fmt, chunk_size)
216 raise NotImplementedError(
217 "Currently only `X` and `raw/X` can be read as sparse."
218 )
220 rdasp = partial(
221 read_dense_as_sparse, sparse_format=as_sparse_fmt, axis_chunk=chunk_size
222 )
--> 224 with h5py.File(filename, "r") as f:
225 d = {}
226 for k in f.keys():
227 # Backwards compat for old raw
File ~/Library/Caches/pypoetry/virtualenvs/standard-workflows-7zflNV5z-py3.9/lib/python3.9/site-packages/h5py/_hl/files.py:533, in File.__init__(self, name, mode, driver, libver, userblock_size, swmr, rdcc_nslots, rdcc_nbytes, rdcc_w0, track_order, fs_strategy, fs_persist, fs_threshold, fs_page_size, page_buf_size, min_meta_keep, min_raw_keep, locking, alignment_threshold, alignment_interval, **kwds)
525 fapl = make_fapl(driver, libver, rdcc_nslots, rdcc_nbytes, rdcc_w0,
526 locking, page_buf_size, min_meta_keep, min_raw_keep,
527 alignment_threshold=alignment_threshold,
528 alignment_interval=alignment_interval,
529 **kwds)
530 fcpl = make_fcpl(track_order=track_order, fs_strategy=fs_strategy,
531 fs_persist=fs_persist, fs_threshold=fs_threshold,
532 fs_page_size=fs_page_size)
--> 533 fid = make_fid(name, mode, userblock_size, fapl, fcpl, swmr=swmr)
535 if isinstance(libver, tuple):
536 self._libver = libver
File ~/Library/Caches/pypoetry/virtualenvs/standard-workflows-7zflNV5z-py3.9/lib/python3.9/site-packages/h5py/_hl/files.py:226, in make_fid(name, mode, userblock_size, fapl, fcpl, swmr)
224 if swmr and swmr_support:
225 flags |= h5f.ACC_SWMR_READ
--> 226 fid = h5f.open(name, flags, fapl=fapl)
227 elif mode == 'r+':
228 fid = h5f.open(name, h5f.ACC_RDWR, fapl=fapl)
File h5py/_objects.pyx:54, in h5py._objects.with_phil.wrapper()
File h5py/_objects.pyx:55, in h5py._objects.with_phil.wrapper()
File h5py/h5f.pyx:106, in h5py.h5f.open()
FileNotFoundError: [Errno 2] Unable to open file (unable to open file: name = 'Users/hanna/Documents/projects/MBEN/all_cnvsNormal/data/all_cnvsNormal.h5ad', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)
class Test(param.Parameterized):
add_data = param.Action(lambda x: x.param.trigger('add_data'), label='Click here!')
number = param.Integer(default=0)
data = ''
@param.depends('add_data')
def _add_data(self):
self.number += 1
self.data = "miau"
import scanpy
self.data = scanpy.read_h5ad('/Users/hanna/Documents/projects/MBEN/all_cnvsNormal/data/all_cnvsNormal.h5ad')
from pathlib import Path
Path('/Users/hanna/Documents/projects/Workflows/standard-workflows/MBEN_T/v00/human/sc/test/data').mkdir(parents=True, exist_ok=True)
#ff = open('/Users/hanna/Documents/projects/Workflows/standard-workflows/MBEN_T/v00/human/sc/test/data/all_cnvsNormal.h5ad', 'w+')
import anndata
self.data.write_h5ad('/Users/hanna/Documents/projects/Workflows/standard-workflows/MBEN_T/v00/human/sc/test/data/all_cnvsNormal.h5ad')
return self.number
test = Test()
pn.Column(
pn.Row(
pn.Column(pn.panel(test, show_name=False, margin=0, widgets={"add_data": {"button_type": "primary"}, "number": {"disabled": True}}),
'**Click the button** to trigger an update in the output.'),
pn.panel(test._add_data, width=300), max_width=600)
)
css = '''
.bk.panel-widget-box {
#background: #fefefe;
border-radius: 5px;
border: 1px black solid;
font-weight: 700;
}
.custom{
background-color: #ffc107;
color: aliceblue;
}
h2{
backgound-color: pink;
}
'''
pn.extension(raw_css=[css])
txt = pn.widgets.TextInput(name = "huhui", placeholder = "huhu")
widget1 = pn.widgets.Button(name = "mybutton")
data = 'huhu'
def my_func(e):
widget1.name = "miau"
txt.value = "muhhh"
data="huihuihui"
print(data)
widget1.on_click(my_func)
ui = pn.panel(pn.Column(widget1, txt))
ui
huihuihui
Comments#
Param:
Param wants to be used in classes?
param.Action button doesn’t allow to add parameters like self etc.?
Using the things in a class somehow doesn’t work. And the error message aren’t presented.
Widgets:
FileInput: Is the filepath saved or only the filename? How do I read a yaml file from io.StringIO??
Button: add on_click event, the attached method must have an event parameter
import anndata
pn.extension(template='fast')
data = anndata.AnnData()
# Basic paramters to set
projName = pn.widgets.TextInput(name = 'Full Project Name', placeholder = 'aNameWithoutSpaces')
projID = pn.widgets.TextInput(name = 'Project ID ', placeholder = 'two to six capital letters')
version = pn.widgets.TextInput(name = 'Analysis Version', placeholder = 'v01')
host = pn.widgets.Select(name = 'Host', options=['human', 'mouse'])
datasetname = pn.widgets.TextInput(name = 'Dataset Name', placeholder = 'all_tumor_liver_pid12pid14')
seqType = pn.widgets.Select(name = 'Sequencing Type', options=['sc', 'sn', 'atac', 'bulk'])
param_editor = pn.widgets.JSONEditor(value= ap.analysis_params, width=400, height=800)
results_folder_path = pn.widgets.TextInput(name = 'Results Folder Path', placeholder = 'path to where to save the results folder')
dataset_source = pn.widgets.TextInput(name = 'Data Filepath')
def _download_params(e):
import yaml
paths = set_paths()
ff = open(paths['analysis_params'], 'w+')
yaml.dump(param_editor.value, ff)
# Buttons
upload_params = pn.widgets.Button(name = 'Upload Parameter File')
download_params = pn.widgets.Button(name='Download Data', button_type='primary')
add_data = pn.widgets.Button(name='Upload Data', button_type='primary')
buttons = pn.Column( 'Upload Parameters', upload_params, download_params, width=300)
def _upload_params(e):
import yaml
from yaml.loader import BaseLoader
paths = set_paths()
with open(paths['analysis_params']) as stream:
# try:
param_editor.value = yaml.load(stream, Loader=BaseLoader)
# except yaml.YAMLError as exc:
# alert_text = ("Please add data first as the project structure with the default analysis_params.yaml file will be generated automatically then.")
# pn.Column(pn.pane.Alert(alert_text.format(alert_type='warning'), alert_type='warning'),sizing_mode='stretch_width')
def _add_data(e):
paths = set_paths()
import scanpy
data = scanpy.read_h5ad(paths['dataset_source'])
from pathlib import Path
Path(paths['dataset_folder']).mkdir(parents=True, exist_ok=True)
data.write_h5ad(paths['dataset_file'])
add_data.on_click(_add_data)
download_params.on_click(_download_params)
upload_params.on_click(_upload_params)
ui = pn.Row(pn.Column('## Basic Project Definition', projName, projID, version, host, datasetname, seqType, pn.layout.Divider(),
'## Upload Dataset', dataset_source, results_folder_path, add_data, pn.layout.Divider(),
'## Up- & Download Parameters', buttons), pn.Spacer(width=100), pn.Column(
'## Adjust Parameters', "If no paramter file is uploaded, default paramters are shown. If you are finished with adjusting them, don't forget to push the download button.",
param_editor, max_width = 400), css_classes=['panel-widget-box']).servable(area='main')
def set_paths() -> dict:
""" Defines basic file & folder paths for receiving and storing data. These paths are needed to initialize the analysis. """
paths = {
'dataset_source' : dataset_source.value,
'dataset_folder' : os.path.join(results_folder_path.value, projID.value, version.value, host.value, seqType.value, datasetname.value, 'data')
}
pahts = paths.update({
'dataset_file': os.path.join(paths['dataset_folder'], 'data.h5ad'),
'analysis_params': os.path.join(results_folder_path.value, projID.value, 'analysis_params.yaml')
})
return paths
# initialize with default values for testing purposes
projName.value, projID.value, version.value, datasetname.value, dataset_source.value, results_folder_path.value = ['MBEN_Test', 'MBEN_T', 'v00', 'test', '/Users/hanna/Documents/projects/MBEN/all_cnvsNormal/data/all_cnvsNormal.h5ad', '/Users/hanna/Documents/projects/Workflows/standard-workflows/docs/']
## Define paths
#pn.serve(pn.Column(pn.pane.Markdown('# Funki').servable(area='sidebar'), ui.servable(area='main')))
template = pn.template.FastListTemplate(
title="Fast Panel App",
logo="https://panel.holoviz.org/_static/logo_stacked.png"
)
m = pn.pane.Markdown('# Funki').servable(area='sidebar')
template.servable()
pn.serve(template, m)
import panel as pn
from panel.template import DarkTheme, DefaultTheme
#css_files = ['./style.css']
#pn.extension(css_files=css_files)
template = pn.template.FastGridTemplate(title='FUNKI', sidebar_footer="hello I'm the footer", theme=DefaultTheme, accent='black')#"#A01346")
template = pn.template.MaterialTemplate(title='FUNKI', sidebar_footer="hello I'm the footer", theme=DefaultTheme, accent='black')#"#A01346")
template = pn.template.BootstrapTemplate(title='FUNKI', sidebar_footer="hello I'm the footer", theme=DefaultTheme, accent='black')#"#A01346")
template = pn.template.VanillaTemplate(title='FUNKI', sidebar_footer="hello I'm the footer", theme=DefaultTheme, accent='black')#"#A01346")
template = pn.template.FastGridTemplate(title='FUNKI', sidebar_footer="hello I'm the footer", theme=DefaultTheme, accent='black')#"#A01346")
template = pn.template.GoldenTemplate(title='FUNKI', sidebar_footer="hello I'm the footer", theme=DefaultTheme, header_background ='black')#"#A01346")
#template = pn.Template(tmpl)
pn.config.sizing_mode = 'stretch_width'
#dashboard side
template.sidebar.append(pn.pane.Markdown("## Settings"))
template.sidebar.append(m)
template.sidebar.append(m)
#dashboard focal
#template.main[:3, :6] = ui
template.main.append(pn.Row(
pn.Card(ui)))
template.main.append(pn.Row(
pn.Card(ui)))
tabs = pn.Tabs(('Scatter', m), ui)
template.main.append(pn.Row(
pn.Card(tabs)))
template.show();
WARNING:param.MaterialTemplate13731: Setting non-parameter attribute sidebar_footer=hello I'm the footer using a mechanism intended only for parameters
WARNING:param.MaterialTemplate13731: Setting non-parameter attribute accent=black using a mechanism intended only for parameters
WARNING:param.BootstrapTemplate13751: Setting non-parameter attribute sidebar_footer=hello I'm the footer using a mechanism intended only for parameters
WARNING:param.BootstrapTemplate13751: Setting non-parameter attribute accent=black using a mechanism intended only for parameters
WARNING:param.VanillaTemplate13771: Setting non-parameter attribute sidebar_footer=hello I'm the footer using a mechanism intended only for parameters
WARNING:param.VanillaTemplate13771: Setting non-parameter attribute accent=black using a mechanism intended only for parameters
WARNING:param.GoldenTemplate13817: Setting non-parameter attribute sidebar_footer=hello I'm the footer using a mechanism intended only for parameters
Launching server at http://localhost:64114
WARNING:tornado.access:404 GET /static/extensions/panel/bundled/jsoneditor/jsoneditor@9.5.6/dist/jsoneditor.map (::1) 3.86ms
pn.extension(..., template="fast")
pn.state.template.param.update(site="Panel", title="FastListTemplate")
m = pn.pane.Markdown("## Settings").servable(target="sidebar")
pn.serve(m)
WARNING:param.panel_extension: Ellipsis extension not recognized and will be skipped.
WARNING:param.panel_extension: A HoloViz extension was loaded previously. This means the extension is already initialized and the following Panel extensions could not be properly loaded: [Ellipsis]. If you are loading custom extensions with pn.extension(...) ensure that this is called before any other HoloViz extension such as hvPlot or HoloViews.
Launching server at http://localhost:55062
<panel.io.server.Server at 0x2998761c0>
WARNING:tornado.access:404 GET /style.css (::1) 9.03ms
WARNING:tornado.access:404 GET /favicon.ico (::1) 0.53ms
import yaml
from yaml.loader import BaseLoader
with open('/Users/hanna/Documents/projects/Workflows/standard-workflows/docs/MBEN_T/analysis_params.yaml') as stream:
d = yaml.load(stream, Loader=BaseLoader)
print(d)
{'default': {'basepaths': {'basepath_binac': '', 'basepath_bioq': '/net/data.isilon/ag-saez/$USER/', 'basepath_local': '/Users/hanna/Documents/', 'localdir': '', 'storagedir': 'mounted'}, 'decoupler': {'meanacts': {'groupby': ['vars'], 'minstd': '0.0'}, 'methods': [['mlm']], 'pseudobulk': {'contrast': [['seurat_clusters', 'CNVs', 'Tumor', 'Normal']], 'sumon': [['PID_CNVs', 'seurat_clusters']], 'test': ['t-test']}}, 'liana': {'base': 'exp(1)', 'lig_rec': [['4', ['3', '1', '2', '0']], ['all']], 'methods': [['natmi', 'connectome', 'logfc', 'sca', 'cellphonedb']]}, 'original_type': 'SeuratObj', 'priorKnowledge': {'dorothea': {'levels': [['A', 'B', 'C']]}}, 'rename': {'clusters': 'seurat_clusters', 'subj_id': 'PID'}}, 'other': {'all': {'comps': {'is_control': ['Tumor', 'Normal']}, 'liana': {'lig_rec': [['all']]}, 'obs_of_interest': ['seurat_clusters', 'CNVs'], 'original_name': 'MB_all_f', 'priorKnowledge': {'dorothea': {}}, 'rename': {'is_control': 'CNVs'}, 'subs': {'CNVs': ['cnvs', ['Normal']], 'seurat_clusters': ['clust', ['5', '6', '7']]}}, 'all_cnvsNormal': {'liana': {'lig_rec': [['all']]}}, 'all_t': {'comps': {'clusters': [['4', ['3', '1']], ['4', '3'], ['3', '1'], ['1', '2'], ['2', '0']]}, 'decoupler': {}, 'obs_of_interest': ['seurat_clusters', 'labels'], 'original_name': 'MB_all_t', 'priorKnowledge': {'dorothea': {}}, 'subs': {'PID': ['subj', ['AK1'], ['AK2'], ['AK3'], ['MB263'], ['MB266'], ['MB287'], ['MB295'], ['MB299'], ['MB88']], 'seurat_clusters': ['clust', ['4', '3', '1', '0', '2'], ['4', '2'], ['4', '1'], ['4', '0']]}}, 'all_t_clust43': {'subs': {'PID': ['subj', ['AK1'], ['AK2'], ['AK3'], ['MB263'], ['MB266'], ['MB287'], ['MB295'], ['MB299'], ['MB88']]}}, 'all_t_clust43102': {'liana': {'lig_rec': [['4', ['3', '1', '2', '0']], ['all']]}, 'subs': {'PID': ['subj', ['AK1'], ['AK2'], ['AK3'], ['MB263'], ['MB266'], ['MB287'], ['MB295'], ['MB299'], ['MB88']]}}}}
import panel as pn
Launching server at http://localhost:50340
<panel.io.server.Server at 0x28d1ae1f0>
analysis_init.proj_data_folder_path
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
Cell In [168], line 1
----> 1 analysis_init.proj_data_folder_path
AttributeError: 'AnalysisInit' object has no attribute 'proj_data_folder_path'
import yaml
m=list(yaml.load(stream.read)
print(m)
[StreamStartEvent(), DocumentStartEvent(), MappingStartEvent(anchor=None, tag=None, implicit=True), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='default'), MappingStartEvent(anchor=None, tag=None, implicit=True), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='basepaths'), MappingStartEvent(anchor=None, tag=None, implicit=True), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='basepath_binac'), ScalarEvent(anchor=None, tag=None, implicit=(False, True), value=''), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='basepath_bioq'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='/net/data.isilon/ag-saez/$USER/'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='basepath_local'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='/Users/hanna/Documents/'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='localdir'), ScalarEvent(anchor=None, tag=None, implicit=(False, True), value=''), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='storagedir'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='mounted'), MappingEndEvent(), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='decoupler'), MappingStartEvent(anchor=None, tag=None, implicit=True), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='meanacts'), MappingStartEvent(anchor=None, tag=None, implicit=True), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='groupby'), SequenceStartEvent(anchor=None, tag=None, implicit=True), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='vars'), SequenceEndEvent(), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='minstd'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='0.0'), MappingEndEvent(), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='methods'), SequenceStartEvent(anchor=None, tag=None, implicit=True), SequenceStartEvent(anchor=None, tag='tag:yaml.org,2002:python/tuple', implicit=False), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='mlm'), SequenceEndEvent(), SequenceEndEvent(), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='pseudobulk'), MappingStartEvent(anchor=None, tag=None, implicit=True), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='contrast'), SequenceStartEvent(anchor=None, tag=None, implicit=True), SequenceStartEvent(anchor=None, tag=None, implicit=True), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='seurat_clusters'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='CNVs'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='Tumor'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='Normal'), SequenceEndEvent(), SequenceEndEvent(), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='sumon'), SequenceStartEvent(anchor=None, tag=None, implicit=True), SequenceStartEvent(anchor=None, tag=None, implicit=True), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='PID_CNVs'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='seurat_clusters'), SequenceEndEvent(), SequenceEndEvent(), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='test'), SequenceStartEvent(anchor=None, tag=None, implicit=True), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='t-test'), SequenceEndEvent(), MappingEndEvent(), MappingEndEvent(), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='liana'), MappingStartEvent(anchor=None, tag=None, implicit=True), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='base'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='exp(1)'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='lig_rec'), SequenceStartEvent(anchor=None, tag=None, implicit=True), SequenceStartEvent(anchor='id012', tag='tag:yaml.org,2002:python/tuple', implicit=False), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='4'), SequenceStartEvent(anchor=None, tag='tag:yaml.org,2002:python/tuple', implicit=False), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='3'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='1'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='2'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='0'), SequenceEndEvent(), SequenceEndEvent(), SequenceStartEvent(anchor='id001', tag='tag:yaml.org,2002:python/tuple', implicit=False), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='all'), SequenceEndEvent(), SequenceEndEvent(), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='methods'), SequenceStartEvent(anchor=None, tag=None, implicit=True), SequenceStartEvent(anchor=None, tag='tag:yaml.org,2002:python/tuple', implicit=False), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='natmi'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='connectome'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='logfc'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='sca'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='cellphonedb'), SequenceEndEvent(), SequenceEndEvent(), MappingEndEvent(), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='original_type'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='SeuratObj'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='priorKnowledge'), MappingStartEvent(anchor=None, tag=None, implicit=True), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='dorothea'), MappingStartEvent(anchor=None, tag=None, implicit=True), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='levels'), SequenceStartEvent(anchor=None, tag=None, implicit=True), SequenceStartEvent(anchor=None, tag='tag:yaml.org,2002:python/tuple', implicit=False), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='A'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='B'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='C'), SequenceEndEvent(), SequenceEndEvent(), MappingEndEvent(), MappingEndEvent(), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='rename'), MappingStartEvent(anchor=None, tag=None, implicit=True), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='clusters'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='seurat_clusters'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='subj_id'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='PID'), MappingEndEvent(), MappingEndEvent(), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='other'), MappingStartEvent(anchor=None, tag=None, implicit=True), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='all'), MappingStartEvent(anchor=None, tag=None, implicit=True), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='comps'), MappingStartEvent(anchor=None, tag=None, implicit=True), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='is_control'), SequenceStartEvent(anchor=None, tag='tag:yaml.org,2002:python/tuple', implicit=False), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='Tumor'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='Normal'), SequenceEndEvent(), MappingEndEvent(), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='liana'), MappingStartEvent(anchor=None, tag=None, implicit=True), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='lig_rec'), SequenceStartEvent(anchor=None, tag=None, implicit=True), AliasEvent(anchor='id001'), SequenceEndEvent(), MappingEndEvent(), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='obs_of_interest'), SequenceStartEvent(anchor=None, tag=None, implicit=True), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='seurat_clusters'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='CNVs'), SequenceEndEvent(), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='original_name'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='MB_all_f'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='priorKnowledge'), MappingStartEvent(anchor=None, tag=None, implicit=True), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='dorothea'), MappingStartEvent(anchor=None, tag=None, implicit=True), MappingEndEvent(), MappingEndEvent(), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='rename'), MappingStartEvent(anchor=None, tag=None, implicit=True), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='is_control'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='CNVs'), MappingEndEvent(), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='subs'), MappingStartEvent(anchor=None, tag=None, implicit=True), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='CNVs'), SequenceStartEvent(anchor=None, tag=None, implicit=True), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='cnvs'), SequenceStartEvent(anchor=None, tag='tag:yaml.org,2002:python/tuple', implicit=False), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='Normal'), SequenceEndEvent(), SequenceEndEvent(), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='seurat_clusters'), SequenceStartEvent(anchor=None, tag=None, implicit=True), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='clust'), SequenceStartEvent(anchor=None, tag='tag:yaml.org,2002:python/tuple', implicit=False), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='5'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='6'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='7'), SequenceEndEvent(), SequenceEndEvent(), MappingEndEvent(), MappingEndEvent(), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='all_cnvsNormal'), MappingStartEvent(anchor=None, tag=None, implicit=True), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='liana'), MappingStartEvent(anchor=None, tag=None, implicit=True), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='lig_rec'), SequenceStartEvent(anchor=None, tag=None, implicit=True), AliasEvent(anchor='id001'), SequenceEndEvent(), MappingEndEvent(), MappingEndEvent(), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='all_t'), MappingStartEvent(anchor=None, tag=None, implicit=True), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='comps'), MappingStartEvent(anchor=None, tag=None, implicit=True), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='clusters'), SequenceStartEvent(anchor=None, tag=None, implicit=True), SequenceStartEvent(anchor=None, tag='tag:yaml.org,2002:python/tuple', implicit=False), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='4'), SequenceStartEvent(anchor='id002', tag='tag:yaml.org,2002:python/tuple', implicit=False), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='3'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='1'), SequenceEndEvent(), SequenceEndEvent(), SequenceStartEvent(anchor=None, tag='tag:yaml.org,2002:python/tuple', implicit=False), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='4'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='3'), SequenceEndEvent(), AliasEvent(anchor='id002'), SequenceStartEvent(anchor=None, tag='tag:yaml.org,2002:python/tuple', implicit=False), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='1'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='2'), SequenceEndEvent(), SequenceStartEvent(anchor=None, tag='tag:yaml.org,2002:python/tuple', implicit=False), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='2'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='0'), SequenceEndEvent(), SequenceEndEvent(), MappingEndEvent(), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='decoupler'), MappingStartEvent(anchor=None, tag=None, implicit=True), MappingEndEvent(), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='obs_of_interest'), SequenceStartEvent(anchor=None, tag=None, implicit=True), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='seurat_clusters'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='labels'), SequenceEndEvent(), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='original_name'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='MB_all_t'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='priorKnowledge'), MappingStartEvent(anchor=None, tag=None, implicit=True), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='dorothea'), MappingStartEvent(anchor=None, tag=None, implicit=True), MappingEndEvent(), MappingEndEvent(), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='subs'), MappingStartEvent(anchor=None, tag=None, implicit=True), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='PID'), SequenceStartEvent(anchor=None, tag=None, implicit=True), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='subj'), SequenceStartEvent(anchor='id003', tag='tag:yaml.org,2002:python/tuple', implicit=False), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='AK1'), SequenceEndEvent(), SequenceStartEvent(anchor='id004', tag='tag:yaml.org,2002:python/tuple', implicit=False), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='AK2'), SequenceEndEvent(), SequenceStartEvent(anchor='id005', tag='tag:yaml.org,2002:python/tuple', implicit=False), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='AK3'), SequenceEndEvent(), SequenceStartEvent(anchor='id006', tag='tag:yaml.org,2002:python/tuple', implicit=False), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='MB263'), SequenceEndEvent(), SequenceStartEvent(anchor='id007', tag='tag:yaml.org,2002:python/tuple', implicit=False), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='MB266'), SequenceEndEvent(), SequenceStartEvent(anchor='id008', tag='tag:yaml.org,2002:python/tuple', implicit=False), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='MB287'), SequenceEndEvent(), SequenceStartEvent(anchor='id009', tag='tag:yaml.org,2002:python/tuple', implicit=False), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='MB295'), SequenceEndEvent(), SequenceStartEvent(anchor='id010', tag='tag:yaml.org,2002:python/tuple', implicit=False), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='MB299'), SequenceEndEvent(), SequenceStartEvent(anchor='id011', tag='tag:yaml.org,2002:python/tuple', implicit=False), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='MB88'), SequenceEndEvent(), SequenceEndEvent(), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='seurat_clusters'), SequenceStartEvent(anchor=None, tag=None, implicit=True), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='clust'), SequenceStartEvent(anchor=None, tag='tag:yaml.org,2002:python/tuple', implicit=False), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='4'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='3'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='1'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='0'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='2'), SequenceEndEvent(), SequenceStartEvent(anchor=None, tag='tag:yaml.org,2002:python/tuple', implicit=False), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='4'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='2'), SequenceEndEvent(), SequenceStartEvent(anchor=None, tag='tag:yaml.org,2002:python/tuple', implicit=False), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='4'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='1'), SequenceEndEvent(), SequenceStartEvent(anchor=None, tag='tag:yaml.org,2002:python/tuple', implicit=False), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='4'), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='0'), SequenceEndEvent(), SequenceEndEvent(), MappingEndEvent(), MappingEndEvent(), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='all_t_clust43'), MappingStartEvent(anchor=None, tag=None, implicit=True), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='subs'), MappingStartEvent(anchor=None, tag=None, implicit=True), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='PID'), SequenceStartEvent(anchor=None, tag=None, implicit=True), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='subj'), AliasEvent(anchor='id003'), AliasEvent(anchor='id004'), AliasEvent(anchor='id005'), AliasEvent(anchor='id006'), AliasEvent(anchor='id007'), AliasEvent(anchor='id008'), AliasEvent(anchor='id009'), AliasEvent(anchor='id010'), AliasEvent(anchor='id011'), SequenceEndEvent(), MappingEndEvent(), MappingEndEvent(), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='all_t_clust43102'), MappingStartEvent(anchor=None, tag=None, implicit=True), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='liana'), MappingStartEvent(anchor=None, tag=None, implicit=True), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='lig_rec'), SequenceStartEvent(anchor=None, tag=None, implicit=True), AliasEvent(anchor='id012'), AliasEvent(anchor='id001'), SequenceEndEvent(), MappingEndEvent(), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='subs'), MappingStartEvent(anchor=None, tag=None, implicit=True), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='PID'), SequenceStartEvent(anchor=None, tag=None, implicit=True), ScalarEvent(anchor=None, tag=None, implicit=(True, False), value='subj'), AliasEvent(anchor='id003'), AliasEvent(anchor='id004'), AliasEvent(anchor='id005'), AliasEvent(anchor='id006'), AliasEvent(anchor='id007'), AliasEvent(anchor='id008'), AliasEvent(anchor='id009'), AliasEvent(anchor='id010'), AliasEvent(anchor='id011'), SequenceEndEvent(), MappingEndEvent(), MappingEndEvent(), MappingEndEvent(), MappingEndEvent(), DocumentEndEvent(), StreamEndEvent()]
@pn.depends('file_name', watch=True)
def _update_filename(self):
self.download.filename = self.file_name
def update_sample_df(self, event=None):
self.analysis_params = ap.analysis_params
@pn.depends("sample_df", watch=True)
def _update_table(self):
if hasattr(self, "table"):
self.table.value = self.sample_df.head(10)
def save_sample_data(self, event=None):
if not self.sample_df is None:
self.sample_df
def view(self):
return pn.Column(
"## Generate and Download Data",
pn.Row(
pn.Param(self, parameters=['generate_sample_df'], show_name=False, widgets={"generate_sample_df": {"button_type": "primary"}}),
pn.Column(self.param.file_name, self.download, align='end', margin=(10,5,5,5)),
),
"**Sample data (10 Rows)**",
self.table,
)
sample_data_app = SampleDataApp()
sample_data_app_view = sample_data_app.view()
sample_data_app_view
Click the Save sample df button
This should save the dataframe to your default download folder. Now let us define the VoltageApp which will display the data we just generated.
class VoltageApp(param.Parameterized):
data = param.DataFrame()
file_input = param.Parameter()
def __init__(self, **params):
super().__init__(file_input=pn.widgets.FileInput(), **params)
self.plotly_pane = pn.pane.Plotly(height=400, sizing_mode="stretch_width")
@pn.depends("file_input.value", watch=True)
def _parse_file_input(self):
value = self.file_input.value
if value:
string_io = io.StringIO(value.decode("utf8"))
self.data = pd.read_csv(string_io, parse_dates=["Time"])
else:
print("error")
@pn.depends('data', watch=True)
def get_plot(self):
df = self.data
if df is None:
return
assert ("Voltage" in df.columns) and ("Time" in df.columns), "no columns voltage and time"
df = (df.loc[df['Voltage'] != 'Invalid/Calib']).copy(deep=True)
df['Voltage'] = df['Voltage'].astype(float)
if "FubId" in df.columns:
p = px.scatter(df, x="Time", y="Voltage", color="FubId")
else:
p = px.scatter(df, x="Time", y="Voltage")
self.plotly_pane.object = p
def view(self):
return pn.Column(
"## Upload and Plot Data",
self.file_input,
self.plotly_pane,
)
voltage_app = VoltageApp()
voltage_app_view = voltage_app.view()
voltage_app_view
Now let us put these two components together into a servable app:
description = """
This application demonstrates the ability to **download** a file using the `FileDownload` widget
and **upload** a file using the `FileInput` widget.
</br></br>
Try filtering the data, download the file by clicking on the Download button
and then plot it on the right by uploading that same file.
"""
component = pn.Column(
description,
#sample_data_app_view,
voltage_app_view,
sizing_mode='stretch_both'
)
component
App#
Lets wrap it into nice template that can be served via panel serve download_upload_csv.ipynb
pn.template.FastListTemplate(site="Panel", title="Download and Upload CSV File", main=[ description,
#sample_data_app_view,
voltage_app_view,]).servable();
pn.serve(component)
Launching server at http://localhost:57395
<panel.io.server.Server at 0x280e77af0>
WARNING:tornado.access:404 GET /favicon.ico (::1) 1.80ms
2022-11-14 16:23:39,277 ERROR: panel.reactive - Callback failed for object named "" changing properties {'filename': 'estimate.csv',
'mime_type': 'text/csv',
'value': b',AHR,AR,ARID2,ARID3A,ARNT,ARNTL,ASCL1,ATF1,ATF2,ATF3,ATF4,ATF6,A'
b'TF7,BACH1,BACH2,BATF,BCL11A,BCL6,BHLHE22,BHLHE40,CDX2,CEBPA,CEBP'
b'B,CEBPD,CEBPG,CLOCK,CREB1,CREB3,CREB3L1,CREM,CTCF,CTCFL,CUX1,DEA'
b'F1,DUX4,E2F1,E2F2,E2F3,E2F4,E2F5,E2F6,E2F7,EBF1,EGR1,EHF,ELF1,EL'
b'F3,ELF5,ELK1,ELK4,EOMES,EPAS1,ERG,ESR1,ESR2,ESRRA,ETS1,ETS2,ETV1'
b',ETV4,ETV6,FLI1,FOS,FOSL1,FOSL2,FOXA1,FOXA2,FOXJ2,FOXK1,FOXK2,FO'
b'XL2,FOXM1,FOXO1,FOXO3,FOXO4,FOXP1,FOXP2,GABPA,GATA1,GATA2,GATA3,'
b'GATA4,GATA6,GFI1B,GLI1,GLI2,GRHL2,HBP1,HES1,HHEX,HIF1A,HINFP,HMB'
b'OX1,HNF1A,HNF1B,HNF4A,HNF4G,HOXA9,HOXB13,HOXB7,HSF1,IKZF1,IRF1,I'
b'RF2,IRF3,IRF4,IRF8,IRF9,JUN,JUNB,JUND,KDM5B,KLF1,KLF13,KLF3,KLF4'
b',KLF5,KLF6,KLF9,KMT2A,KMT2B,LEF1,LHX2,LYL1,MAF,MAFB,MAFF,MAFG,MA'
b'FK,MAX,MAZ,MBD1,MBD2,MEF2A,MEF2B,MEF2C,MEIS1,MEIS2,MITF,MNT,MXI1'
b',MYB,MYBL2,MYC,MYCN,MYOD1,NANOG,NCOA1,NCOA2,NCOA3,NEUROD1,NFATC1'
b',NFATC2,NFE2,NFE2L1,NFE2L2,NFIC,NFKB1,NFKB2,NFYA,NFYB,NR1H2,NR1H'
b'3,NR1H4,NR1I2,NR2C2,NR2F1,NR2F2,NR2F6,NR3C1,NR4A1,NR5A1,NR5A2,NR'
b'F1,ONECUT1,OTX2,PAX5,PAX6,PAX8,PBX2,PBX3,PDX1,PGR,PKNOX1,POU2F1,'
b'POU2F2,POU4F2,POU5F1,PPARA,PPARG,PRDM1,PRDM14,PROX1,RARA,RARB,RA'
b'RG,RBPJ,REL,RELA,RELB,REST,RFX1,RFX2,RFX5,RUNX1,RUNX2,RUNX3,RXRA'
b',RXRB,SATB1,SIX2,SIX5,SMAD1,SMAD3,SMAD4,SMAD5,SNAI1,SNAI2,SNAPC4'
b',SOX10,SOX11,SOX13,SOX2,SOX6,SOX9,SP1,SP2,SP3,SP4,SPI1,SPIB,SREB'
b'F1,SREBF2,SRF,STAT1,STAT2,STAT3,STAT4,STAT5A,STAT5B,STAT6,TAL1,T'
b'BP,TBX21,TCF12,TCF3,TCF4,TCF7,TCF7L2,TEAD1,TEAD2,TEAD4,TFAP2A,TF'
b'AP2C,TFAP4,TFDP1,TGIF2,THAP1,THAP11,TP53,TP63,TP73,TWIST1,USF1,U'
b'SF2,VDR,WT1,XBP1,YBX1,YY1,ZBED1,ZBTB11,ZBTB33,ZBTB7A,ZC3H8,ZEB1,'
b'ZEB2,ZFX,ZHX1,ZHX2,ZKSCAN1,ZNF143,ZNF197,ZNF217,ZNF24,ZNF263,ZNF'
b'274,ZNF384,ZNF584,ZNF592,ZNF639,ZNF644,ZNF740\nICGC_MB287_c2,-2.0'
b'50912,-1.5246949,2.2493024,-1.6781397,2.1968977,-0.5588189,3.185'
b'288,-1.0926898,0.10588172,-1.0021957,0.88791615,2.4416416,1.5599'
b'017,0.16850127,2.029054,-0.20166305,3.074538,-0.21408378,2.31908'
b'15,-0.14213462,1.7597896,0.9976135,0.5109422,1.0980518,-3.292858'
b',0.36268768,-0.0083131045,1.021776,1.537372,-2.203738,3.583133,2'
b'.0941508,-0.35281697,-0.30161655,-0.94813764,1.2072501,-0.235970'
b'66,-0.6697394,0.80083424,1.1284096,1.3543801,-0.5529994,-2.68359'
b'07,2.8471837,-0.75591284,0.9535374,-0.08669024,-0.05474908,0.595'
b'69776,-0.15393747,3.8363204,-2.2363265,-0.95350516,-0.29894608,1'
b'.6943884,2.01955,-0.9140117,-0.35592434,1.0133438,-0.9081534,-1.'
b'6999193,-0.337918,-0.4938888,0.48163274,0.04998806,4.7393513,-0.'
b'466359,2.9480376,2.4540522,0.279386,0.32415783,-0.25565404,-1.11'
b'37123,-1.615564,-0.6577288,7.232973,-0.94127303,5.0728226,-1.642'
b'2235,3.7338395,3.622676,-0.61311203,0.58628666,2.9766076,-0.2600'
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